Abstract: Internal control, a series of internal adjustment methods and supervision measures that aim at meeting the goals of various operational activities inside the organizations, can be divided into internal management control and internal accountant control. It plays a major role in lowering the risks and increasing the benefits. Institutions of higher learning shoulder the responsibilities of talent training, science research and social services, therefore there are internal requirements as well as external requirements for establishing Internal Control System in institutions of higher learning. This paper focuses on the effect and benefits of input and output in institutions of higher learning, and analyzes the framework and content of Internal Control System establishment.